AutoCloner

Multiple sequence alignment - TraesCS2A01G067000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS2A01G067000	chr2A	100.000	3141	0	0	1	3141	30081632	30078492	0.000000e+00	5801.0
1	TraesCS2A01G067000	chr2A	91.001	1389	98	15	780	2150	30087031	30085652	0.000000e+00	1847.0
2	TraesCS2A01G067000	chr2A	89.446	1355	86	27	807	2150	30091857	30090549	0.000000e+00	1657.0
3	TraesCS2A01G067000	chr2A	92.932	665	31	11	1494	2150	30126893	30126237	0.000000e+00	953.0
4	TraesCS2A01G067000	chr2A	88.317	796	57	17	23	791	30089395	30088609	0.000000e+00	922.0
5	TraesCS2A01G067000	chr2A	88.301	359	25	8	807	1162	30127450	30127106	6.270000e-112	414.0
6	TraesCS2A01G067000	chr2A	100.000	28	0	0	1	28	81591075	81591102	6.000000e-03	52.8
7	TraesCS2A01G067000	chr2D	94.506	2166	81	12	23	2160	27890038	27887883	0.000000e+00	3306.0
8	TraesCS2A01G067000	chr2D	91.808	1355	92	10	807	2150	27892473	27891127	0.000000e+00	1869.0
9	TraesCS2A01G067000	chr2D	88.768	828	54	16	1350	2150	27902332	27901517	0.000000e+00	977.0
10	TraesCS2A01G067000	chr2D	95.707	396	17	0	1747	2142	27853945	27853550	3.420000e-179	638.0
11	TraesCS2A01G067000	chr2D	95.619	388	17	0	1755	2142	27860340	27859953	9.570000e-175	623.0
12	TraesCS2A01G067000	chr2D	92.891	422	30	0	1721	2142	27883781	27883360	5.760000e-172	614.0
13	TraesCS2A01G067000	chr2D	81.586	782	94	26	67	809	27900627	27899857	4.480000e-168	601.0
14	TraesCS2A01G067000	chr2D	87.290	417	51	2	1725	2140	27849563	27849148	2.830000e-130	475.0
15	TraesCS2A01G067000	chr2D	88.301	359	25	8	807	1162	27902739	27902395	6.270000e-112	414.0
16	TraesCS2A01G067000	chr2B	90.192	1356	112	12	807	2150	44353056	44351710	0.000000e+00	1748.0
17	TraesCS2A01G067000	chr2B	91.515	990	70	12	2158	3141	59694886	59693905	0.000000e+00	1351.0
18	TraesCS2A01G067000	chr2B	90.498	863	59	13	736	1581	44348022	44347166	0.000000e+00	1118.0
19	TraesCS2A01G067000	chr2B	88.915	839	49	21	1350	2150	44361617	44360785	0.000000e+00	994.0
20	TraesCS2A01G067000	chr2B	93.043	575	31	6	1580	2150	44347062	44346493	0.000000e+00	832.0
21	TraesCS2A01G067000	chr2B	87.248	745	50	18	23	740	44350601	44349875	0.000000e+00	808.0
22	TraesCS2A01G067000	chr2B	94.853	408	20	1	1744	2150	44274408	44274001	1.230000e-178	636.0
23	TraesCS2A01G067000	chr2B	84.874	357	27	9	807	1154	44362020	44361682	5.020000e-88	335.0
24	TraesCS2A01G067000	chr2B	92.537	134	10	0	676	809	44344333	44344200	3.200000e-45	193.0
25	TraesCS2A01G067000	chr2B	100.000	28	0	0	1	28	691192602	691192629	6.000000e-03	52.8
26	TraesCS2A01G067000	chr2B	100.000	28	0	0	1	28	766619463	766619436	6.000000e-03	52.8
27	TraesCS2A01G067000	chr7A	98.571	980	13	1	2159	3138	626254296	626255274	0.000000e+00	1731.0
28	TraesCS2A01G067000	chr7A	99.339	756	5	0	2386	3141	60707048	60706293	0.000000e+00	1369.0
29	TraesCS2A01G067000	chr5A	97.660	983	21	2	2159	3141	568867087	568866107	0.000000e+00	1687.0
30	TraesCS2A01G067000	chr4B	92.929	990	56	10	2159	3138	577676398	577677383	0.000000e+00	1428.0
31	TraesCS2A01G067000	chr4A	92.675	983	62	5	2159	3138	623594415	623595390	0.000000e+00	1408.0
32	TraesCS2A01G067000	chr4A	88.956	987	94	13	2161	3138	666781059	666780079	0.000000e+00	1205.0
33	TraesCS2A01G067000	chr7B	90.707	990	82	8	2159	3141	660915096	660914110	0.000000e+00	1310.0
34	TraesCS2A01G067000	chr6D	90.178	957	87	7	2185	3138	372540413	372541365	0.000000e+00	1240.0
35	TraesCS2A01G067000	chr5B	87.691	983	117	4	2159	3138	548652947	548653928	0.000000e+00	1142.0
36	TraesCS2A01G067000	chr5B	92.487	386	27	2	1758	2142	300097907	300097523	4.580000e-153	551.0
37	TraesCS2A01G067000	chr5D	92.746	386	26	2	1758	2142	266325770	266325386	9.840000e-155	556.0
38	TraesCS2A01G067000	chr5D	91.067	403	30	6	1745	2142	266086047	266086448	9.910000e-150	540.0
39	TraesCS2A01G067000	chr1D	80.702	171	29	3	1180	1348	478341776	478341608	2.540000e-26	130.0
40	TraesCS2A01G067000	chr1A	77.876	226	36	9	66	290	550598290	550598078	9.140000e-26	128.0
41	TraesCS2A01G067000	chr6B	100.000	28	0	0	1	28	67933222	67933249	6.000000e-03	52.8
42	TraesCS2A01G067000	chr3D	100.000	28	0	0	1	28	2581311	2581338	6.000000e-03	52.8

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS2A01G067000	chr2A	30078492	30081632	3140	True	5801.000000	5801	100.000000	1	3141	1	chr2A.!!$R1	3140
1	TraesCS2A01G067000	chr2A	30085652	30091857	6205	True	1475.333333	1847	89.588000	23	2150	3	chr2A.!!$R2	2127
2	TraesCS2A01G067000	chr2A	30126237	30127450	1213	True	683.500000	953	90.616500	807	2150	2	chr2A.!!$R3	1343
3	TraesCS2A01G067000	chr2D	27887883	27892473	4590	True	2587.500000	3306	93.157000	23	2160	2	chr2D.!!$R4	2137
4	TraesCS2A01G067000	chr2D	27899857	27902739	2882	True	664.000000	977	86.218333	67	2150	3	chr2D.!!$R5	2083
5	TraesCS2A01G067000	chr2D	27849148	27853945	4797	True	556.500000	638	91.498500	1725	2142	2	chr2D.!!$R3	417
6	TraesCS2A01G067000	chr2B	59693905	59694886	981	True	1351.000000	1351	91.515000	2158	3141	1	chr2B.!!$R2	983
7	TraesCS2A01G067000	chr2B	44344200	44353056	8856	True	939.800000	1748	90.703600	23	2150	5	chr2B.!!$R4	2127
8	TraesCS2A01G067000	chr2B	44360785	44362020	1235	True	664.500000	994	86.894500	807	2150	2	chr2B.!!$R5	1343
9	TraesCS2A01G067000	chr7A	626254296	626255274	978	False	1731.000000	1731	98.571000	2159	3138	1	chr7A.!!$F1	979
10	TraesCS2A01G067000	chr7A	60706293	60707048	755	True	1369.000000	1369	99.339000	2386	3141	1	chr7A.!!$R1	755
11	TraesCS2A01G067000	chr5A	568866107	568867087	980	True	1687.000000	1687	97.660000	2159	3141	1	chr5A.!!$R1	982
12	TraesCS2A01G067000	chr4B	577676398	577677383	985	False	1428.000000	1428	92.929000	2159	3138	1	chr4B.!!$F1	979
13	TraesCS2A01G067000	chr4A	623594415	623595390	975	False	1408.000000	1408	92.675000	2159	3138	1	chr4A.!!$F1	979
14	TraesCS2A01G067000	chr4A	666780079	666781059	980	True	1205.000000	1205	88.956000	2161	3138	1	chr4A.!!$R1	977
15	TraesCS2A01G067000	chr7B	660914110	660915096	986	True	1310.000000	1310	90.707000	2159	3141	1	chr7B.!!$R1	982
16	TraesCS2A01G067000	chr6D	372540413	372541365	952	False	1240.000000	1240	90.178000	2185	3138	1	chr6D.!!$F1	953
17	TraesCS2A01G067000	chr5B	548652947	548653928	981	False	1142.000000	1142	87.691000	2159	3138	1	chr5B.!!$F1	979

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
427	2926	1.237285	ACGACATGTGAAAGCTGGGC	61.237	55.000	1.15	0.0	0.0	5.36	F
1455	5835	1.532868	GCACATAGGCAAAGCTATCCG	59.467	52.381	0.00	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1927	6445	0.179000	ATCGACCGTCGTAGTACCCT	59.821	55.000	19.89	0.0	41.35	4.34	R
2384	6903	3.056891	CCACGTCAAGCCCATTTTTGTAT	60.057	43.478	0.00	0.0	0.00	2.29	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
94	2590	9.127277	TCAGCACCTACAAAAATTACTAAGTTT	57.873	29.630	0.00	0.00	0.00	2.66
196	2694	7.561237	AAATATTTGCATTCACGTGTACAAC	57.439	32.000	16.51	3.55	0.00	3.32
368	2866	4.871557	CCAACACATTTAATTCCATGGCAG	59.128	41.667	6.96	0.00	0.00	4.85
421	2920	8.843733	CATTCTCAATTAAACGACATGTGAAAG	58.156	33.333	1.15	0.00	30.36	2.62
422	2921	6.370593	TCTCAATTAAACGACATGTGAAAGC	58.629	36.000	1.15	0.00	0.00	3.51
424	2923	6.142139	TCAATTAAACGACATGTGAAAGCTG	58.858	36.000	1.15	0.00	0.00	4.24
427	2926	1.237285	ACGACATGTGAAAGCTGGGC	61.237	55.000	1.15	0.00	0.00	5.36
441	2965	1.549203	CTGGGCTTGGCTTATTGTGT	58.451	50.000	0.00	0.00	0.00	3.72
463	2987	2.203280	CGCTTCACCCACCCAACA	60.203	61.111	0.00	0.00	0.00	3.33
487	3011	2.354196	GCGTGCGAATGAGTATTTTCG	58.646	47.619	0.00	1.00	45.61	3.46
577	3101	4.891756	AGGAATAGGAAAATGCCACATCTG	59.108	41.667	0.00	0.00	0.00	2.90
582	3106	5.121380	AGGAAAATGCCACATCTGATACT	57.879	39.130	0.00	0.00	0.00	2.12
734	3258	4.623002	TGTTCGTAACTAATGCAGTGACA	58.377	39.130	0.00	0.00	38.43	3.58
792	4906	2.671963	GGGGTCTTTCCGTGGCAC	60.672	66.667	7.79	7.79	37.00	5.01
1066	5436	1.550130	CCAGGGGCTTAAGTCGACCA	61.550	60.000	13.01	0.00	0.00	4.02
1088	5458	4.883354	CCTTCCCATCAGCCGCCC	62.883	72.222	0.00	0.00	0.00	6.13
1184	5554	9.683069	GAATATTATTTTTGCGAAGGATGATGT	57.317	29.630	0.00	0.00	0.00	3.06
1400	5776	4.075963	AGCTGGCATGAATGTTTTTGTT	57.924	36.364	0.00	0.00	0.00	2.83
1455	5835	1.532868	GCACATAGGCAAAGCTATCCG	59.467	52.381	0.00	0.00	0.00	4.18
1473	5858	3.792736	TAGGACGCCCACATGCCC	61.793	66.667	0.00	0.00	33.88	5.36
1716	6234	6.428465	GCCTTATTATGGCTAGGTCTTTCTTC	59.572	42.308	12.21	0.00	46.38	2.87
1879	6397	3.511610	AAGTGGGTGCCCTGCCTT	61.512	61.111	8.91	5.40	36.94	4.35
1966	6484	2.664402	ACTGGACAATGTGGAAGCTT	57.336	45.000	0.00	0.00	0.00	3.74
2059	6577	0.179084	CCTATGTCCGCGTCATTGGT	60.179	55.000	22.81	5.98	34.95	3.67
2297	6815	2.703536	TGACAACTGTACCACCATGACT	59.296	45.455	0.00	0.00	0.00	3.41
2384	6903	2.481276	CGTCATGGATTTGGAGACGCTA	60.481	50.000	0.00	0.00	44.21	4.26
2576	7419	8.752187	ACACAATTAATTCTATTGAACATGCCT	58.248	29.630	16.07	0.00	36.67	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	3.508012	CCCCGTGATCTCTACTCCTAATG	59.492	52.174	0.00	0.00	0.00	1.90
10	11	3.140519	ACCCCGTGATCTCTACTCCTAAT	59.859	47.826	0.00	0.00	0.00	1.73
11	12	2.512896	ACCCCGTGATCTCTACTCCTAA	59.487	50.000	0.00	0.00	0.00	2.69
12	13	2.133520	ACCCCGTGATCTCTACTCCTA	58.866	52.381	0.00	0.00	0.00	2.94
13	14	0.927767	ACCCCGTGATCTCTACTCCT	59.072	55.000	0.00	0.00	0.00	3.69
14	15	1.033574	CACCCCGTGATCTCTACTCC	58.966	60.000	0.00	0.00	35.23	3.85
15	16	1.033574	CCACCCCGTGATCTCTACTC	58.966	60.000	0.00	0.00	35.23	2.59
16	17	0.397254	CCCACCCCGTGATCTCTACT	60.397	60.000	0.00	0.00	35.23	2.57
17	18	2.029307	GCCCACCCCGTGATCTCTAC	62.029	65.000	0.00	0.00	35.23	2.59
19	20	3.083997	GCCCACCCCGTGATCTCT	61.084	66.667	0.00	0.00	35.23	3.10
20	21	4.176752	GGCCCACCCCGTGATCTC	62.177	72.222	0.00	0.00	35.23	2.75
94	2590	6.917477	GTCAAAATGCAAACTGACATTACTGA	59.083	34.615	16.32	0.00	38.43	3.41
181	2679	5.845953	GTCATTTCAGTTGTACACGTGAATG	59.154	40.000	25.01	17.07	0.00	2.67
187	2685	5.845985	ATCAGTCATTTCAGTTGTACACG	57.154	39.130	0.00	0.00	0.00	4.49
196	2694	9.045223	TCGACCAAAATATATCAGTCATTTCAG	57.955	33.333	0.00	0.00	0.00	3.02
293	2791	1.315257	GGGCTAGTTGTGGTGGCATG	61.315	60.000	0.00	0.00	0.00	4.06
368	2866	3.134804	CCCCATATAGTATAGCAGCCCAC	59.865	52.174	0.00	0.00	0.00	4.61
421	2920	0.174162	CACAATAAGCCAAGCCCAGC	59.826	55.000	0.00	0.00	0.00	4.85
422	2921	1.203052	CACACAATAAGCCAAGCCCAG	59.797	52.381	0.00	0.00	0.00	4.45
424	2923	0.532115	CCACACAATAAGCCAAGCCC	59.468	55.000	0.00	0.00	0.00	5.19
427	2926	1.131126	CGCTCCACACAATAAGCCAAG	59.869	52.381	0.00	0.00	0.00	3.61
431	2955	0.804989	AAGCGCTCCACACAATAAGC	59.195	50.000	12.06	0.00	0.00	3.09
441	2965	4.329545	GGTGGGTGAAGCGCTCCA	62.330	66.667	12.06	11.59	41.54	3.86
487	3011	5.871396	TCTTCATATAGGTTCCACAGTCC	57.129	43.478	0.00	0.00	0.00	3.85
490	3014	8.567285	AAAACTTCTTCATATAGGTTCCACAG	57.433	34.615	0.00	0.00	0.00	3.66
554	3078	4.891756	CAGATGTGGCATTTTCCTATTCCT	59.108	41.667	0.00	0.00	0.00	3.36
555	3079	4.889409	TCAGATGTGGCATTTTCCTATTCC	59.111	41.667	0.00	0.00	0.00	3.01
556	3080	6.645790	ATCAGATGTGGCATTTTCCTATTC	57.354	37.500	0.00	0.00	0.00	1.75
634	3158	9.334947	AGTCATCCATACTCTTATGTTTCATTG	57.665	33.333	0.00	0.00	34.27	2.82
722	3246	7.774625	TCATCCAAATCTAATGTCACTGCATTA	59.225	33.333	0.00	0.00	39.50	1.90
734	3258	8.951614	ATCACCATTGATCATCCAAATCTAAT	57.048	30.769	0.00	0.00	38.08	1.73
761	3285	5.648960	GGAAAGACCCCAAAACGTCATATAA	59.351	40.000	0.00	0.00	0.00	0.98
792	4906	4.774200	AGAGGGGTGGAAAATCAAAATGAG	59.226	41.667	0.00	0.00	0.00	2.90
1066	5436	4.115199	GCTGATGGGAAGGCCGGT	62.115	66.667	1.90	0.00	33.83	5.28
1112	5482	2.031919	TTCCGCCATTGCTGACGT	59.968	55.556	0.00	0.00	29.81	4.34
1184	5554	0.324614	ACGATGATGTGCCTTGACCA	59.675	50.000	0.00	0.00	0.00	4.02
1400	5776	6.097554	ACCCGATAAATTAATCAATTGTGGCA	59.902	34.615	5.13	0.00	34.53	4.92
1455	5835	2.513897	GGCATGTGGGCGTCCTAC	60.514	66.667	7.97	6.52	33.57	3.18
1473	5858	1.081242	GTGATGCACAGTTTGGCCG	60.081	57.895	0.00	0.00	34.08	6.13
1552	5952	9.781834	GTACACATTGGAATAAAATCGATTTCA	57.218	29.630	22.93	10.23	32.27	2.69
1660	6174	8.731275	TTACTCCTTATGTCCATACATTTGTG	57.269	34.615	0.00	0.00	44.07	3.33
1716	6234	6.361481	CACAATTGATCAACACTTAGTGCTTG	59.639	38.462	13.59	14.86	36.98	4.01
1879	6397	0.183492	AGCCAACCTTGCTGAACTCA	59.817	50.000	0.00	0.00	37.76	3.41
1927	6445	0.179000	ATCGACCGTCGTAGTACCCT	59.821	55.000	19.89	0.00	41.35	4.34
1966	6484	0.249120	CAGTGCACCCGAACATAGGA	59.751	55.000	14.63	0.00	0.00	2.94
2059	6577	1.573932	CTGGCGCATGTTGTCGAAA	59.426	52.632	10.83	0.00	0.00	3.46
2384	6903	3.056891	CCACGTCAAGCCCATTTTTGTAT	60.057	43.478	0.00	0.00	0.00	2.29
2618	7461	6.443792	CACGTTTTAAAAGGGCTTTACTCAT	58.556	36.000	21.13	0.00	31.63	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.